Designing a validation application for genetic and genomic evaluation systems in the New Zealand dairy industry

Abstract

New Zealand Animal Evaluation Limited (NZAEL) is considering a transition from their pedigree-based genetic evaluation system to a single-step genomic evaluation system, both of which use BOLT and Helical software. Central to the successful implementation of this system is a robust validation process that ensures the reliability of genomic breeding values (GEBVs) compared to current traditional estimated breeding values (EBVs). To accomplish this task, NZAEL and AbacusBio began a collaborative project to design an automated validation pipeline and accompanying R Shiny application. The objective was to create a tool that efficiently assesses the performance of the new genomic evaluation system across more than 30 traits, focusing on flexibility, minimal user intervention, and applicability to various stakeholder needs. The design process began with a facilitated workshop aimed at defining the project’s scope. Key outcomes included the identification of critical validation analyses and metrics, criteria for evaluating (G)EBV performance, and the selection of relevant focal groups for the initial validation. This approach prioritized the needs of preliminary stakeholders, while also considering the broader interests of the New Zealand dairy sector. A significant aspect of the project was differentiating between 'routine' validation analyses, which would be directly integrated into the application, and 'exploratory' analyses, which required additional resources. This distinction allowed for a more focused development effort and a clearer understanding of the project's deliverables. The result of this collaboration was a validation application that streamlines the identification of problems and communication with stakeholders. Our experience underscores the importance of a user-centric design process in developing scientific tools, highlighting the need for clear communication, stakeholder engagement, and flexibility in project management.